Align Acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate WP_011384931.1 AMB_RS12840 thiamine pyrophosphate protein
Query= curated2:Q7U5G1 (617 letters) >NCBI__GCF_000009985.1:WP_011384931.1 Length = 561 Score = 244 bits (624), Expect = 5e-69 Identities = 174/521 (33%), Positives = 260/521 (49%), Gaps = 31/521 (5%) Query: 17 APQTISGAAALMDALRRHGVDTIFGYPGGAILPIYDALHIAESEGWVKHILVRHEQAGTH 76 AP+T G L DAL G DT+ PG + LP DA + +K + RHE + Sbjct: 7 APRT--GGEILADALLAQGADTVTCVPGESFLPFLDAAW--DRRDRLKVLAFRHEGGAAY 62 Query: 77 AADAYARATGKVGVCFGTSGPGATNLVTGIATAQMDSVPMVVITGQVPRPAIGTDAFQET 136 AA+A+ + TG+ GVC GPGAT+ G+ TA DS PMV++ GQV RP G +AFQE Sbjct: 63 AAEAHGKLTGRPGVCIVGRGPGATHASVGVHTAFQDSTPMVLLIGQVDRPIRGREAFQEV 122 Query: 137 DIFGITLPIVKHSWVVRDPADLGSIVAQAFLIAASGRPGPVLIDIPKDVGQEQFNYVPVE 196 ++ + P+ K + P L VA+AF A GRPGP ++ +P+D+ E+ + VE Sbjct: 123 ELAQMFRPLAKRVEEITSPDRLPEAVARAFAAAMGGRPGPAVLILPEDMLAERASVADVE 182 Query: 197 PGSVIPGGFHQPEPPLDAAVAAALDLIEQAQRPLLYVGGGAISACAHDSLRMLAERYQLP 256 +P P P + ++L+ +A+RPL+ VGGG + A + AE + LP Sbjct: 183 R---LPPALPHPGP---CRLDKMVELLAKARRPLMLVGGGGWTPEAARLITAFAEGWSLP 236 Query: 257 VTTTLMGKGAFDENDALSVGMLGMHGTAYANFAVTECDLLIAVGARFDDRVT---GKLDT 313 V + D A G LG V E DL++AVG R D T ++ Sbjct: 237 VAACFRRQDIVDNESACYGGELGYSMAPSLGARVREADLILAVGTRLGDIDTAGYSLIEA 296 Query: 314 FAPRARVVHFEIDPAEIGKNRKADVAVLGDLGLSLARMVEISLQRTAEPRTAAWLE---- 369 P+ ++H + E+G+ + D+A++ + L AR + A P W + Sbjct: 297 PNPKQILIHVFPEAEELGRVFRPDLAIVSAM-LPFARRA----SQLAAPAALPWTDWTRA 351 Query: 370 -RINTWKDRYPLTIPPAEGAIYPQEVLLAVRDLAP-DAIVTTDVGQHQMWAAQ-HLRNGP 426 R + +R P + P GA+ +V+ + P DAI+ T G + W + H Sbjct: 352 VRGDHLANRVPNSCP---GALDMGQVMAEIEARLPEDAIICTGAGNYTGWPQRFHRFRRY 408 Query: 427 RGWISSAGLGTMGFGMPAAMGAQVAMPDRQVVCIAGDASILMNIQELGTLAAYGLPVKVV 486 G ++ A G+MG+G+PAA+ A+ PDR VV AGD LM QEL T +GL V+ Sbjct: 409 PGQLAPAN-GSMGYGLPAALAAKALYPDRAVVAFAGDGCFLMTAQELATAKLHGLSPVVL 467 Query: 487 IVNNHWQGMVRQWQESFYDERYSASDMLNGMPDFIALARSF 527 +V+N G +R QE+ + R A+D+ N PDF ALA ++ Sbjct: 468 VVDNGMYGTIRMHQEASHPGRTLATDLAN--PDFAALAAAY 506 Lambda K H 0.320 0.136 0.414 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 948 Number of extensions: 46 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 617 Length of database: 561 Length adjustment: 37 Effective length of query: 580 Effective length of database: 524 Effective search space: 303920 Effective search space used: 303920 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 53 (25.0 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory